This study aimed to obtain the genetic parameters of gynogenetic ENU-induced mutagenesis in grass carp (). The relative DNA content in grass carp with ENU-induced mutagenesis (Q group) and gynogenetic ENU-induced mutagenesis (E group) was 24.02 and 23.80, respectively. The Partec CyFlow ploidy analyzer determined that the values were close and that the mutants were diploid. We selected 28 microsatellite markers to investigate the genetic diversity of the two carp groups. Respectively, the E and Q groups had average alleles of 3.7143 and 5.1786, average effective alleles of 2.1857 and 4.0028, average expected homozygosity of 0.5122 and 0.2814, average expected heterozygosity of 0.4878 and 0.7186, and average polymorphism information content (PIC) of 0.4282 and 0.6606. The homozygous rate analysis of microsatellite loci indicated that the E group did not contain completely homozygous individuals, as all exhibited a degree of purity <1.00. The analysis also showed that homozygosity in several microsatellite loci (including , HLJC118) improved significantly at different rates. In summary, meiotic gynogenesis of ENU-induced mutagenic grass carp improved microsatellite homozygosity at different rates and significantly decreased genetic diversity. Thus, this method yields highly homozygous individuals that can provide important genetic data for improved selection of ENU-induced mutagenic grass carp.